Arthur Weber - Academia.edu (original) (raw)

Papers by Arthur Weber

As shown in Figure 1, abiogenesis has several requirements: (A) a source of organic substrates an... more As shown in Figure 1, abiogenesis has several requirements: (A) a source of organic substrates and chemical energy that drives the synthesis of (B) useful small molecules (ammonia, monomers, metabolites, energy molecules), and (C) a second synthetic processs that yields large replicating and catalytic polymers that control (D) the growth and maintenance of a primitive protocell. Furthermore, the required chemical energy must be sustained and effectively coupled to individual reactions to drive biosynthesis at a rate that counters chemical degradation. Energy coupling would have been especially difficult during the origin of life before the development of powerful enzyme catalysts with 3-D active sites. To solve this energy coupling problem we have investigated abiogenesis using sugar substrates whose energized carbon groups drive spontaneous synthetic self-transformation reactions that yield: biometabolites, catalytic molecules, energy-rich thioesters, amino acids, plausible alterna...

Introduction: Past studies of prebiotic peptide bond synthesis have generally been carried out in... more Introduction: Past studies of prebiotic peptide bond synthesis have generally been carried out in the acidic to neutral pH range [1, 2]. Here we report a new process for peptide bond (amide) synthesis in the neutral to alkaline pH range that involves simple dry-down heating of amino acids in the presence of glycerol and bicarbonate. Glycerol was included in the reaction mixture as a solvent and to provide hydroxyl groups for possible formation of ester intermediates previously implicated in peptide bond synthesis under acidic to neutral conditions [1]. Bicarbonate was added to raise the reaction pH to 8-9. Results: Our early studies showed that dry-down condensation at 90°C of α-L-alanine in the presence of glycerol and bicarbonate gave high yields of dialanine and cyclic dialanine with a small amount of alanine trimer and tetramer. Both glycerol and bicarbonate were required for peptide bond synthesis. Apparently, the synthesis of long peptides by α-alanine is blocked by efficient ...

Astrobiology, 2007

Stable, hydrogen-burning, M dwarf stars make up about 75% of all stars in the Galaxy. They are ex... more Stable, hydrogen-burning, M dwarf stars make up about 75% of all stars in the Galaxy. They are extremely long-lived, and because they are much smaller in mass than the Sun (between 0.5 and 0.08 M Sun), their temperature and stellar luminosity are low and peaked in the red. We have reexamined what is known at present about the potential for a terrestrial planet forming within, or migrating into, the classic liquid-surface-water habitable zone close to an

Journal of The American Society for Mass Spectrometry, 2015

Full characterization of complex reaction mixtures is necessary to understand mechanisms, optimiz... more Full characterization of complex reaction mixtures is necessary to understand mechanisms, optimize yields, and elucidate secondary reaction pathways. Molecular-level information for species in such mixtures can be readily obtained by coupling mass spectrometry imaging (MSI) with thin layer chromatography (TLC) separations. User-guided investigation of imaging data for mixture components with known m/z values is generally straightforward; however, spot detection for unknowns is highly tedious, and limits the applicability of MSI in conjunction with TLC. To accelerate imaging data mining, we developed DetectTLC, an approach that automatically identifies m/z values exhibiting TLC spot-like regions in MS molecular images. Furthermore, DetectTLC can also spatially match m/z values for spots acquired during alternating high and low collision-energy scans, pairing product ions with precursors to enhance structural identification. As an example, DetectTLC is applied to the identification and structural confirmation of unknown, yet significant, products of abiotic pyrazinone and aminopyrazine nucleoside analog synthesis.

Origins of Life and Evolution of Biospheres

Origins of Life and Evolution of Biospheres

Origins of Life and Evolution of the Biosphere

The thermodynamics of organic chemistry under mild aqueous conditions was examined in order to be... more The thermodynamics of organic chemistry under mild aqueous conditions was examined in order to begin to understand its influence on the structure and operation of metabolism and its antecedents. Free energies (deltaG) were estimated for four types of reactions of biochemical importance carbon-carbon bond cleavage and synthesis, hydrogen transfer between carbon groups, dehydration of alcohol groups, and aldo-keto isomerization. The energies were calculated for mainly aliphatic groups composed of carbon, hydrogen, and oxygen. The energy values showed (1) that generally when carbon-carbon bond cleavage involves groups from different functional group classes (i.e., carboxylic acids, carbonyl groups, alcohols, and hydrocarbons), the transfer of the shared electron-pair to the more reduced carbon group is energetically favored over transfer to the more oxidized carbon group, and (2) that the energy of carbon-carbon bond transformation is primarily determined by the functional group class of the group that changes oxidation state in the reaction (i.e., the functional group class of the group that donates the shared electron-pair during cleavage, or that accepts the incipient shared electron-pair during synthesis). In contrast, the energy of hydrogen transfer between carbon groups is determined by the functional group class of both the hydrogen-donor group and the hydrogen-acceptor group. From these and other observations we concluded that the chemistry involved in the origin of metabolism (and to a lesser degree modern metabolism) was strongly constrained by (1) the limited redox-based transformation energy of organic substrates that is readily dissipated in a few energetically favorable irreversible reactions; (2) the energy dominance of a few transformation half-reactions that determines whether carbon-carbon bond transformation (cleavage or synthesis) is energetically favorable (deltaG < -3.5 kcal/mol), reversible (deltaG between +/-3.5 kcal/mol), or unfavorable (deltaG > +3.5 kcal/mol); and (3) the dependence of carbon group transformation energy on the functional group class (i.e., oxidation state) of participating groups that in turn is contingent on prior reactions and precursors in the synthetic pathway.

J Mol Evol, 1985

Alanine is formed under anaerobic conditions from glyceraldehyde and ammonium ion in aqueous solu... more Alanine is formed under anaerobic conditions from glyceraldehyde and ammonium ion in aqueous solutions of sodium phosphate (pH 7.0) or imidazole-imidazo|ium chloride (pH 7.(3) at ambient temperature. In 500 mM imidazole (pH 7.0), alanine synthesis from 10 mM glyceraldehyde and 15 mM ammonium ion is roughly 6 times more rapid in the presence of 10 mM 3-mercaptopropionate (0.62% yield at 60 days) than in its absence (0.10% yield at 60 days). Likewise, the formation of alanine in 500 mM sodium phosphate (pH 7.0) from 5 mM glyceraldehyde and 10 mM ammonium ion is more rapid in the presence of 10 mM Nacetylcysteine than in its absence. In this reaction with N-acetylcysteine, the ratio of the yield of alanine to the yield of lactate is fairly constant. The yield ofalanine is about 4.5% that of lactate. Alanine synthesis in the presence of thiol probably proceeds via alanyl thioester, which is produced by rearrangement of the imine of the hemithioacetal of pyruvaldehyde, a product of glyceraldehyde dehydration. The significance of this reaction for molecular evolution is discussed.

Journal of Molecular Evolution, Feb 1, 1991

The primitiveness of contemporary fatty acid biosynthesis was evaluated by using the thermodynami... more The primitiveness of contemporary fatty acid biosynthesis was evaluated by using the thermodynamics and kinetics of its component reactions to estimate the extent of its dependence on powerful and selective catalysis by enzymes. Since this analysis indicated that the modem pathway is not primitive because it requires sophisticated enzymatic catalysis, we here propose an alternative pathway of primitive fatty acid synthesis that uses glycolaldehyde as a substrate. In contrast to the modem pathway, this primitive pathway is not dependent on an exogenous source of phosphoanhydride energy (ATP). Furthermore, the chemical spontaneity of its reactions suggests that it could have been readily catalyzed by the rudimentary biocatalysts available at an early stage in the origin of life.

Origins of Life and Evolution of the Biosphere, 2010

Glycolaldehyde and DL-glyceraldehyde reacted in a water-buffered solution under mildly acidic con... more Glycolaldehyde and DL-glyceraldehyde reacted in a water-buffered solution under mildly acidic conditions and in the presence of chiral dipeptide catalysts produced pentose sugars whose configuration is affected by the chirality of the catalyst. The chiral effect was found to vary between catalysts and to be largest for di-valine. Lyxose, arabinose, ribose and xylose are formed in different amounts, whose relative proportions do not change significantly with the varying of conditions. With LL-peptide catalysts, ribose was the only pentose sugar to have a significant D-enantiomeric excess (ee) (≤44%), lyxose displayed an Lee of ≤66%, arabinose a smaller Lee of ≤8%, and xylose was about racemic. These data expand our previous findings for tetrose sugars and further substantiate the suggestion that interactions between simple molecules of prebiotic relevance on the early Earth might have included the transfer of chiral asymmetry and advanced molecular evolution.

J Mol Evol, 1978

Amino acids are activated by reaction with adenosine 5'-phosphorimidazolide in aqueous im... more Amino acids are activated by reaction with adenosine 5'-phosphorimidazolide in aqueous imidazole buffers. If adenosine 5'-(O-methylphosphate), an analogue of the 3'-terminus of t-RNA is present, 2'(3')-O-aminoacyladenosine 5'-(O-methylphosphate) is formed. Fifteen percent of this compound accumulated at pH 5.8, but less was formed at higher pHs. The highest efficiency of utilization if ImpA attained in our experiments was about 24%. Analogous reactions occured with several other amino acids, including a number that have functional side-chains.

J Mol Evol, 1980

The self-condensation of 2'(3')-O-glycyl esters of adenosine, adenosine-5'-(O-methylphosphate) an... more The self-condensation of 2'(3')-O-glycyl esters of adenosine, adenosine-5'-(O-methylphosphate) and P1, P2-diadenosine-5'-pyrophosphate in 6.2 mM solutions at pH 8.0 and-5 ° C in the presence of 12.5 mM poly(U) yields approximately 3 times as much diketopiperazine as reactions without poly(U). As the concentration of 2'(3')-O-(glycyl)-P1, P2-diadenosine-5'-pyrophosphate is decreased from 6.2 mM to 1.5 mM the yield of diketopiperazine in the presence of poly(U) decreases slightly from 6.6% to 5.2%, whereas, in the absence of poly(U) the yield of diketopiperazine decreases substantially from 2.4% to 0.75%. The enhanced yield of diketopiperazine that is attributed to the template action of poly(U) is temperature dependent and is observed only at temperatures below 10 ° C (5 ° C to-5 ° C) for 6.2 mM 2'(3')-O-(glycyl)-adenosine-5'-(O-methylphosphate) and below 23 ° C (15 o C to-5 ° C) for 6.2 mM 2'(3')-O-(glycyl)-P1, P2-diadenosine-5'-pyrophosphate. The absence of a template effect at high temperatures is attributed to the melting of the organized helices. The hydrolysis half-lives at pH 8.0 and-5 ° C of 2'(3')-O-(glycyl)-adenosine, 2'(3')-O-(glycyl)-adeno sine-5'-(O-met hylphosphat e), 2'(3')-O-(glycyl)-P 1, P2-diadenosine-5'-pyrophosphate, and 5'-O-(glycyl)-adenosine in the presence of poly(U) are substantially larger than their half-lives in the absence of poly(U). The condensation of 2'(3')-O-(glycyl)-adenosine yields 5% of 5'-O-(glycyl)adenosine in the presence of poly(U) compared to 0.7% in the absence of poly(U).

Origins Life Evol Biosphere, 1987

Abstracl. Glyceraldehyde acts as a source of energy and monomers in a new model of the origin of ... more Abstracl. Glyceraldehyde acts as a source of energy and monomers in a new model of the origin of life. The simplest form of the model functions by converting formaldehyde from the environment into glyceraldehyde which spontaneously forms hemiacetal adducts that are oxidized to polyglyceric acid. Polyglyceric acid, in turn, acts as an autocatalyst with a rudimentary replicating ability. A unique property of the model is its ability to unite the origin of metabolism and the origin of polymer synthesis into a single process. Furthermore, the chemical resemblance of the model to glycolysis gives it the potential to develop a biological metabolism in a straightforward manner.

[

Journal of Molecular Evolution, Feb 1, 1987

Reaction of DL-serine and adenosine-5-phosphorimidazolide in the presence of adenosine-5'... more Reaction of DL-serine and adenosine-5-phosphorimidazolide in the presence of adenosine-5'-(O-methylphosphate) and imidazole resulted in the stereoselective synthesis of the aminoacyl nucleotide ester 2'(3')-O-seryl-adenosine-5'-(O-methylphosphate). The enantiomeric excess of D-serine incorporated into 2'(3')-O-seryl-adenosine-5'-(O-methylphosphate) was about 9%. Adenylyl-(5'----N)-serine and an unknown product also incorporated an excess of D-serine; however, serylserine showed an excess of L-serine. The relationship of these results to the origin of the biological pairing of L-amino acids and nucleotides containing D-ribose is discussed.

Origins of Life and Evolution of the Biosphere, Jul 1, 1998

Formaldehyde and glycolaldehyde (substrates of the formose autocatalytic cycle) were shown to rea... more Formaldehyde and glycolaldehyde (substrates of the formose autocatalytic cycle) were shown to react with ammonia yielding alanine and homoserine under mild aqueous conditions in the presence of thiol catalysts. Since similar reactions carried out without ammonia yielded α-hydroxy acid thioesters (Weber, 1984a, b), the thiol-dependent synthesis of alanine and homoserine is presumed to occur via amino acid thioesters-intermediates capable of forming peptides (Weber and Orgel 1979). A pH 5.2 solution of 20 mM formaldehyde, 20 mM glycolaldehyde, 20 mM ammonium chloride, 23 mM 3-mercaptopropionic acid, and 23 mM acetic acid that reacted for 35 days at 40 • C yielded (based on initial formaldehyde) 1.8% alanine and 0.08% homoserine. In the absence of thiol catalyst, the synthesis of alanine and homoserine was negligible. Alanine synthesis required both formaldehyde and glycolaldehyde, but homoserine synthesis required only glycolaldehyde. At 25 days the efficiency of alanine synthesis calculated from the ratio of alanine synthesized to formaldehyde reacted was 2.1%, and the yield (based on initial formaldehyde) of triose and tetrose intermediates involved in alanine and homoserine synthesis was 0.3 and 2.1%, respectively. Alanine synthesis was also seen in similar reactions containing only 10 mM each of aldehyde substrates, ammonia, and thiol. The prebiotic significance of these reactions that use the formose reaction to generate sugar intermediates that are converted to reactive amino acid thioesters is discussed.

Origins Life Evol Biosphere, 1995

The oxidation of 2,3-dimercapto-1-propanol by ferric ions on the surface of iron(III) hydroxide o... more The oxidation of 2,3-dimercapto-1-propanol by ferric ions on the surface of iron(III) hydroxide oxide (Fe(OH)O) yielded polydisulfide oligomers. This polymerization occurred readily at low dithiol concentration under mild aqueous conditions. Polydisulfide polymers up to the 15-mer were synthesized from 1 mM dithiol in 5 ml water reacted with iron(III) hydroxide oxide (20 mg, 160 micromoles Fe) for 3 days under anaerobic conditions at 40 degrees C and pH 4. About 91% of the dithiol was converted to short soluble oligomers and 9% to insoluble larger oligomers that were isolated with the Fe(OH)O phase. Reactions carried out at the same ratio of dithiol to Fe(OH)O but at higher dithiol concentrations gave higher yields of the larger insoluble oligomers. The relationship of these results to prebiotic polymer synthesis is discussed.

As shown in Figure 1, abiogenesis has several requirements: (A) a source of organic substrates an... more As shown in Figure 1, abiogenesis has several requirements: (A) a source of organic substrates and chemical energy that drives the synthesis of (B) useful small molecules (ammonia, monomers, metabolites, energy molecules), and (C) a second synthetic processs that yields large replicating and catalytic polymers that control (D) the growth and maintenance of a primitive protocell. Furthermore, the required chemical energy must be sustained and effectively coupled to individual reactions to drive biosynthesis at a rate that counters chemical degradation. Energy coupling would have been especially difficult during the origin of life before the development of powerful enzyme catalysts with 3-D active sites. To solve this energy coupling problem we have investigated abiogenesis using sugar substrates whose energized carbon groups drive spontaneous synthetic self-transformation reactions that yield: biometabolites, catalytic molecules, energy-rich thioesters, amino acids, plausible alterna...

Introduction: Past studies of prebiotic peptide bond synthesis have generally been carried out in... more Introduction: Past studies of prebiotic peptide bond synthesis have generally been carried out in the acidic to neutral pH range [1, 2]. Here we report a new process for peptide bond (amide) synthesis in the neutral to alkaline pH range that involves simple dry-down heating of amino acids in the presence of glycerol and bicarbonate. Glycerol was included in the reaction mixture as a solvent and to provide hydroxyl groups for possible formation of ester intermediates previously implicated in peptide bond synthesis under acidic to neutral conditions [1]. Bicarbonate was added to raise the reaction pH to 8-9. Results: Our early studies showed that dry-down condensation at 90°C of α-L-alanine in the presence of glycerol and bicarbonate gave high yields of dialanine and cyclic dialanine with a small amount of alanine trimer and tetramer. Both glycerol and bicarbonate were required for peptide bond synthesis. Apparently, the synthesis of long peptides by α-alanine is blocked by efficient ...

Astrobiology, 2007

Stable, hydrogen-burning, M dwarf stars make up about 75% of all stars in the Galaxy. They are ex... more Stable, hydrogen-burning, M dwarf stars make up about 75% of all stars in the Galaxy. They are extremely long-lived, and because they are much smaller in mass than the Sun (between 0.5 and 0.08 M Sun), their temperature and stellar luminosity are low and peaked in the red. We have reexamined what is known at present about the potential for a terrestrial planet forming within, or migrating into, the classic liquid-surface-water habitable zone close to an

Journal of The American Society for Mass Spectrometry, 2015

Full characterization of complex reaction mixtures is necessary to understand mechanisms, optimiz... more Full characterization of complex reaction mixtures is necessary to understand mechanisms, optimize yields, and elucidate secondary reaction pathways. Molecular-level information for species in such mixtures can be readily obtained by coupling mass spectrometry imaging (MSI) with thin layer chromatography (TLC) separations. User-guided investigation of imaging data for mixture components with known m/z values is generally straightforward; however, spot detection for unknowns is highly tedious, and limits the applicability of MSI in conjunction with TLC. To accelerate imaging data mining, we developed DetectTLC, an approach that automatically identifies m/z values exhibiting TLC spot-like regions in MS molecular images. Furthermore, DetectTLC can also spatially match m/z values for spots acquired during alternating high and low collision-energy scans, pairing product ions with precursors to enhance structural identification. As an example, DetectTLC is applied to the identification and structural confirmation of unknown, yet significant, products of abiotic pyrazinone and aminopyrazine nucleoside analog synthesis.

Origins of Life and Evolution of Biospheres

Origins of Life and Evolution of Biospheres

Origins of Life and Evolution of the Biosphere

The thermodynamics of organic chemistry under mild aqueous conditions was examined in order to be... more The thermodynamics of organic chemistry under mild aqueous conditions was examined in order to begin to understand its influence on the structure and operation of metabolism and its antecedents. Free energies (deltaG) were estimated for four types of reactions of biochemical importance carbon-carbon bond cleavage and synthesis, hydrogen transfer between carbon groups, dehydration of alcohol groups, and aldo-keto isomerization. The energies were calculated for mainly aliphatic groups composed of carbon, hydrogen, and oxygen. The energy values showed (1) that generally when carbon-carbon bond cleavage involves groups from different functional group classes (i.e., carboxylic acids, carbonyl groups, alcohols, and hydrocarbons), the transfer of the shared electron-pair to the more reduced carbon group is energetically favored over transfer to the more oxidized carbon group, and (2) that the energy of carbon-carbon bond transformation is primarily determined by the functional group class of the group that changes oxidation state in the reaction (i.e., the functional group class of the group that donates the shared electron-pair during cleavage, or that accepts the incipient shared electron-pair during synthesis). In contrast, the energy of hydrogen transfer between carbon groups is determined by the functional group class of both the hydrogen-donor group and the hydrogen-acceptor group. From these and other observations we concluded that the chemistry involved in the origin of metabolism (and to a lesser degree modern metabolism) was strongly constrained by (1) the limited redox-based transformation energy of organic substrates that is readily dissipated in a few energetically favorable irreversible reactions; (2) the energy dominance of a few transformation half-reactions that determines whether carbon-carbon bond transformation (cleavage or synthesis) is energetically favorable (deltaG < -3.5 kcal/mol), reversible (deltaG between +/-3.5 kcal/mol), or unfavorable (deltaG > +3.5 kcal/mol); and (3) the dependence of carbon group transformation energy on the functional group class (i.e., oxidation state) of participating groups that in turn is contingent on prior reactions and precursors in the synthetic pathway.

J Mol Evol, 1985

Alanine is formed under anaerobic conditions from glyceraldehyde and ammonium ion in aqueous solu... more Alanine is formed under anaerobic conditions from glyceraldehyde and ammonium ion in aqueous solutions of sodium phosphate (pH 7.0) or imidazole-imidazo|ium chloride (pH 7.(3) at ambient temperature. In 500 mM imidazole (pH 7.0), alanine synthesis from 10 mM glyceraldehyde and 15 mM ammonium ion is roughly 6 times more rapid in the presence of 10 mM 3-mercaptopropionate (0.62% yield at 60 days) than in its absence (0.10% yield at 60 days). Likewise, the formation of alanine in 500 mM sodium phosphate (pH 7.0) from 5 mM glyceraldehyde and 10 mM ammonium ion is more rapid in the presence of 10 mM Nacetylcysteine than in its absence. In this reaction with N-acetylcysteine, the ratio of the yield of alanine to the yield of lactate is fairly constant. The yield ofalanine is about 4.5% that of lactate. Alanine synthesis in the presence of thiol probably proceeds via alanyl thioester, which is produced by rearrangement of the imine of the hemithioacetal of pyruvaldehyde, a product of glyceraldehyde dehydration. The significance of this reaction for molecular evolution is discussed.

Journal of Molecular Evolution, Feb 1, 1991

The primitiveness of contemporary fatty acid biosynthesis was evaluated by using the thermodynami... more The primitiveness of contemporary fatty acid biosynthesis was evaluated by using the thermodynamics and kinetics of its component reactions to estimate the extent of its dependence on powerful and selective catalysis by enzymes. Since this analysis indicated that the modem pathway is not primitive because it requires sophisticated enzymatic catalysis, we here propose an alternative pathway of primitive fatty acid synthesis that uses glycolaldehyde as a substrate. In contrast to the modem pathway, this primitive pathway is not dependent on an exogenous source of phosphoanhydride energy (ATP). Furthermore, the chemical spontaneity of its reactions suggests that it could have been readily catalyzed by the rudimentary biocatalysts available at an early stage in the origin of life.

Origins of Life and Evolution of the Biosphere, 2010

Glycolaldehyde and DL-glyceraldehyde reacted in a water-buffered solution under mildly acidic con... more Glycolaldehyde and DL-glyceraldehyde reacted in a water-buffered solution under mildly acidic conditions and in the presence of chiral dipeptide catalysts produced pentose sugars whose configuration is affected by the chirality of the catalyst. The chiral effect was found to vary between catalysts and to be largest for di-valine. Lyxose, arabinose, ribose and xylose are formed in different amounts, whose relative proportions do not change significantly with the varying of conditions. With LL-peptide catalysts, ribose was the only pentose sugar to have a significant D-enantiomeric excess (ee) (≤44%), lyxose displayed an Lee of ≤66%, arabinose a smaller Lee of ≤8%, and xylose was about racemic. These data expand our previous findings for tetrose sugars and further substantiate the suggestion that interactions between simple molecules of prebiotic relevance on the early Earth might have included the transfer of chiral asymmetry and advanced molecular evolution.

J Mol Evol, 1978

Amino acids are activated by reaction with adenosine 5'-phosphorimidazolide in aqueous im... more Amino acids are activated by reaction with adenosine 5'-phosphorimidazolide in aqueous imidazole buffers. If adenosine 5'-(O-methylphosphate), an analogue of the 3'-terminus of t-RNA is present, 2'(3')-O-aminoacyladenosine 5'-(O-methylphosphate) is formed. Fifteen percent of this compound accumulated at pH 5.8, but less was formed at higher pHs. The highest efficiency of utilization if ImpA attained in our experiments was about 24%. Analogous reactions occured with several other amino acids, including a number that have functional side-chains.

J Mol Evol, 1980

The self-condensation of 2'(3')-O-glycyl esters of adenosine, adenosine-5'-(O-methylphosphate) an... more The self-condensation of 2'(3')-O-glycyl esters of adenosine, adenosine-5'-(O-methylphosphate) and P1, P2-diadenosine-5'-pyrophosphate in 6.2 mM solutions at pH 8.0 and-5 ° C in the presence of 12.5 mM poly(U) yields approximately 3 times as much diketopiperazine as reactions without poly(U). As the concentration of 2'(3')-O-(glycyl)-P1, P2-diadenosine-5'-pyrophosphate is decreased from 6.2 mM to 1.5 mM the yield of diketopiperazine in the presence of poly(U) decreases slightly from 6.6% to 5.2%, whereas, in the absence of poly(U) the yield of diketopiperazine decreases substantially from 2.4% to 0.75%. The enhanced yield of diketopiperazine that is attributed to the template action of poly(U) is temperature dependent and is observed only at temperatures below 10 ° C (5 ° C to-5 ° C) for 6.2 mM 2'(3')-O-(glycyl)-adenosine-5'-(O-methylphosphate) and below 23 ° C (15 o C to-5 ° C) for 6.2 mM 2'(3')-O-(glycyl)-P1, P2-diadenosine-5'-pyrophosphate. The absence of a template effect at high temperatures is attributed to the melting of the organized helices. The hydrolysis half-lives at pH 8.0 and-5 ° C of 2'(3')-O-(glycyl)-adenosine, 2'(3')-O-(glycyl)-adeno sine-5'-(O-met hylphosphat e), 2'(3')-O-(glycyl)-P 1, P2-diadenosine-5'-pyrophosphate, and 5'-O-(glycyl)-adenosine in the presence of poly(U) are substantially larger than their half-lives in the absence of poly(U). The condensation of 2'(3')-O-(glycyl)-adenosine yields 5% of 5'-O-(glycyl)adenosine in the presence of poly(U) compared to 0.7% in the absence of poly(U).

Origins Life Evol Biosphere, 1987

Abstracl. Glyceraldehyde acts as a source of energy and monomers in a new model of the origin of ... more Abstracl. Glyceraldehyde acts as a source of energy and monomers in a new model of the origin of life. The simplest form of the model functions by converting formaldehyde from the environment into glyceraldehyde which spontaneously forms hemiacetal adducts that are oxidized to polyglyceric acid. Polyglyceric acid, in turn, acts as an autocatalyst with a rudimentary replicating ability. A unique property of the model is its ability to unite the origin of metabolism and the origin of polymer synthesis into a single process. Furthermore, the chemical resemblance of the model to glycolysis gives it the potential to develop a biological metabolism in a straightforward manner.

[

Journal of Molecular Evolution, Feb 1, 1987

Reaction of DL-serine and adenosine-5-phosphorimidazolide in the presence of adenosine-5'... more Reaction of DL-serine and adenosine-5-phosphorimidazolide in the presence of adenosine-5'-(O-methylphosphate) and imidazole resulted in the stereoselective synthesis of the aminoacyl nucleotide ester 2'(3')-O-seryl-adenosine-5'-(O-methylphosphate). The enantiomeric excess of D-serine incorporated into 2'(3')-O-seryl-adenosine-5'-(O-methylphosphate) was about 9%. Adenylyl-(5'----N)-serine and an unknown product also incorporated an excess of D-serine; however, serylserine showed an excess of L-serine. The relationship of these results to the origin of the biological pairing of L-amino acids and nucleotides containing D-ribose is discussed.

Origins of Life and Evolution of the Biosphere, Jul 1, 1998

Formaldehyde and glycolaldehyde (substrates of the formose autocatalytic cycle) were shown to rea... more Formaldehyde and glycolaldehyde (substrates of the formose autocatalytic cycle) were shown to react with ammonia yielding alanine and homoserine under mild aqueous conditions in the presence of thiol catalysts. Since similar reactions carried out without ammonia yielded α-hydroxy acid thioesters (Weber, 1984a, b), the thiol-dependent synthesis of alanine and homoserine is presumed to occur via amino acid thioesters-intermediates capable of forming peptides (Weber and Orgel 1979). A pH 5.2 solution of 20 mM formaldehyde, 20 mM glycolaldehyde, 20 mM ammonium chloride, 23 mM 3-mercaptopropionic acid, and 23 mM acetic acid that reacted for 35 days at 40 • C yielded (based on initial formaldehyde) 1.8% alanine and 0.08% homoserine. In the absence of thiol catalyst, the synthesis of alanine and homoserine was negligible. Alanine synthesis required both formaldehyde and glycolaldehyde, but homoserine synthesis required only glycolaldehyde. At 25 days the efficiency of alanine synthesis calculated from the ratio of alanine synthesized to formaldehyde reacted was 2.1%, and the yield (based on initial formaldehyde) of triose and tetrose intermediates involved in alanine and homoserine synthesis was 0.3 and 2.1%, respectively. Alanine synthesis was also seen in similar reactions containing only 10 mM each of aldehyde substrates, ammonia, and thiol. The prebiotic significance of these reactions that use the formose reaction to generate sugar intermediates that are converted to reactive amino acid thioesters is discussed.

Origins Life Evol Biosphere, 1995

The oxidation of 2,3-dimercapto-1-propanol by ferric ions on the surface of iron(III) hydroxide o... more The oxidation of 2,3-dimercapto-1-propanol by ferric ions on the surface of iron(III) hydroxide oxide (Fe(OH)O) yielded polydisulfide oligomers. This polymerization occurred readily at low dithiol concentration under mild aqueous conditions. Polydisulfide polymers up to the 15-mer were synthesized from 1 mM dithiol in 5 ml water reacted with iron(III) hydroxide oxide (20 mg, 160 micromoles Fe) for 3 days under anaerobic conditions at 40 degrees C and pH 4. About 91% of the dithiol was converted to short soluble oligomers and 9% to insoluble larger oligomers that were isolated with the Fe(OH)O phase. Reactions carried out at the same ratio of dithiol to Fe(OH)O but at higher dithiol concentrations gave higher yields of the larger insoluble oligomers. The relationship of these results to prebiotic polymer synthesis is discussed.